[Biopython] Assembly db

[Peter Cock]

Hi Mark,

This looks like a limitation on the NCBI side. You'll have to email
the NCBI Entrez help - but please let us know what they say.

Thanks,

Peter

On Thu, Sep 15, 2016 at 5:18 PM, Mark Nadel <mark.e.nadel at gmail.com> wrote:
> I’m trying to interrogate the Assembly db using BioPython, in particular
> Entrez.eqquerry.
>
> Here is a short sample:
>
> from Bio import Entrez
> Entrez.email = “mark.e.nadel at gmail.com"
> handle = Entrez.egquery(term="human")
> record = Entrez.read(handle)
> for row in record["eGQueryResult"]:
>    print(row["DbName"], row["Count"])
>
>
> Here is what it returned:
>
> pubmed 16538765
> pmc 2632118
> mesh 15606
> books 121016
> pubmedhealth 15915
> omim 16423
> ncbisearch 2108
> nuccore 24393071
> nucgss 2822763
> nucest 10464214
> protein 15851328
> genome 1462
> structure 54639
> taxonomy 1
> snp 164994517
> dbvar 4986177
> gene 3003185
> sra 859530
> biosystems 26219
> unigene 11917
> cdd 2383
> clone 17567234
> popset 35669
> geoprofiles 64608705
> gds 1196509
> homologene 18907
> pccompound 1356
> pcsubstance 68984
> pcassay 384781
> nlmcatalog 104253
> probe 27886166
> gap 53517
> proteinclusters 20
> bioproject 42794
> biosample 2631235
>
> Note that there is no entry for the Assembly db. I have noticed using other
> queries that a value of 0 is possible for a db.
>
> Can anyone help me with this issue?
>
> Thanks,
>
> Mark
>
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